Universes

• UnitCell
  • Creating simulation cell
  • Indexing simulation cell
  • Boundary conditions and cells
  • Distances and cells
• Topology
  • Atom type
  • Topology
  • Periodic table information
• Frame
• Interactions
  • Using non-default computation
• Potentials
  • Potential functions
  • Potential computation

Universe type

The Universe type contains data about a simulation. In order to build an universe, you can use the following functions.

Universe(cell, topology)

Create a new universe with the simulation cell cell and the Topology topology.

setframe!(universe, frame)

Set the Frame of universe to frame.

setcell!(universe, cell)

Set the simulation cell of universe to cell.

setcell!(universe, [celltype, ]paremeters...)

Set the simulation cell of universe to UnitCell(parameters..., celltype).

add_atom!(u::Universe, atom::Atom)

Add the Atom atom to the universe topology.

add_liaison!(u::Universe, atom_i::Atom, atom_j::Atom)

Add a liaison between the atoms at indexes i and j in the universe topology.

remove_atom!(u::Universe, index)

Remove the atom at index i in the universe topology.

remove_liaison!(u::Universe, atom_i::Atom, atom_j::Atom)

Remove any liaison between the atoms at indexes i and j in the universe topology.

The add_interaction!() function is already documented in the Interactions section of this document.

Loading initial configurations from files

It is often usefull to load initial configurations from files, instead of building it by hand. The Trajectories module provides functionalities for this.